In my case, I knew we can deviate the first leg and do the final check in at the gate. That fact that it let me do the final check in at the gate reinforced my thinking that that’s simply what you do to let CRS know what you are doing. I didn’t know was that you had to uncheck the box for the second leg. In fact, I never notice me those check boxes before this incident. I looked in the new hire guide again and see where the confusion comes from as it doesn’t specify exactly what you are supposed to do in this situation. Lesson learned, luckily for me it was a non-issue with the DO.